Merge pull request #2 from RMI-PACTA/feat/1-enable-report-generation

Feat/1 enable report generation

.github/workflows/build-Docker-image-nightly.yml

@@ -0,0 +1,12 @@
+on:
+  schedule:
+    - cron:  '0 0 * * 1,2,3,4,5'
+
+jobs:
+  build_docker_image:
+    name: "Call build and push action"
+    uses: ./.github/workflows/build-and-push-Docker-image.yml
+    secrets: inherit
+    with:
+      image-name: workflow.pacta.report
+      image-tag: nightly

.github/workflows/build-Docker-image-on-push-to-main.yml

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+on:
+  push:
+    branches: [main]
+
+jobs:
+  build_docker_image:
+    name: "Call build and push action"
+    uses: ./.github/workflows/build-and-push-Docker-image.yml
+    secrets: inherit
+    with:
+      image-name: workflow.pacta.report
+      image-tag: main

.github/workflows/build-Docker-image-on-push-to-pr.yml

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+on:
+  pull_request:
+
+jobs:
+  build_docker_image:
+    name: "Call build and push action"
+    uses: ./.github/workflows/build-and-push-Docker-image.yml
+    secrets: inherit
+    with:
+      image-name: workflow.pacta.report
+      image-tag: pr${{ github.event.pull_request.number }}
+
+  add_comment:
+    needs: build_docker_image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Find Comment
+        # https://github.com/peter-evans/find-comment
+        uses: peter-evans/find-comment@v2
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: Docker image from this PR
+
+      - name: Create or update comment
+        # https://github.com/peter-evans/create-or-update-comment
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            Docker image from this PR (${{ github.event.pull_request.head.sha }}) created
+            ```
+            docker pull ${{ needs.build_docker_image.outputs.full-image-name }}
+            ```
+          edit-mode: replace

.github/workflows/build-and-push-Docker-image.yml

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+---
+name: Build and push docker image
+
+on:
+  workflow_call:
+    inputs:
+      image-name:
+        required: true
+        type: string
+      image-tag:
+        required: true
+        type: string
+    outputs:
+      full-image-name:
+        description: "Full pushed image name including host/registry, name, and tag"
+        value: ${{ jobs.docker.outputs.full-image-name }}
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+    timeout-minutes: 25
+    outputs:
+      full-image-name: ${{ steps.image-name.outputs.full-image-name }}
+
+    steps:
+
+      - name: Define image name
+        id: image-name
+        run: |
+          full_image_name="ghcr.io/${{ github.repository_owner }}/${{ inputs.image-name }}:${{ inputs.image-tag }}"
+          full_image_name=$(echo $full_image_name | tr '[A-Z]' '[a-z]')
+          echo "full-image-name=$full_image_name" >> "$GITHUB_OUTPUT"
+          echo "$full_image_name" > full-image-name
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: full-image-name
+          path: .
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          push: true
+          tags: ${{ steps.image-name.outputs.full-image-name }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=min
+          no-cache-filters: install-pacta
+
+  check-system-dependencies:
+    name: "Check System Dependencies"
+    needs: docker
+    uses: ./.github/workflows/check-R-sysdeps.yml
+    with:
+      image: ${{ needs.docker.outputs.full-image-name }}

.github/workflows/check-R-sysdeps.yml

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+---
+name: Check R system dependencies
+
+on:
+  workflow_call:
+    inputs:
+      image:
+        required: true
+        type: string
+
+jobs:
+
+  check-system-dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Pull image'
+        run: |
+          echo ${{ inputs.image }}
+          docker pull ${{ inputs.image }}
+      - name: 'Run pak::sysreqs_check_installed()'
+        run: |
+
+          docker run \
+          --rm \
+          --entrypoint "/bin/sh" \
+          ${{ inputs.image }} \
+          -c "Rscript -e '
+            x <- pak::sysreqs_check_installed()
+            print(x)
+            is_installed <- as.data.frame(x)[[\"installed\"]]
+            stopifnot(all(is_installed))
+          '"

.github/workflows/run-hadolint.yml

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+---
+on: [push, pull_request]
+
+jobs:
+  hadolint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: hadolint/[email protected]
+        with:
+          dockerfile: Dockerfile

DESCRIPTION

@@ -0,0 +1,11 @@
+Type: PACTA
+Description: Run PACTA.
+Depends:
+  dplyr,
+  fs,
+  jsonlite,
+  logger,
+  pacta.executive.summary,
+  pacta.portfolio.report,
+  pacta.portfolio.utils,
+  readr

Dockerfile

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+# using rocker r-vers as a base with R 4.3.1
+# https://hub.docker.com/r/rocker/r-ver
+# https://rocker-project.org/images/versioned/r-ver.html
+#
+# sets CRAN repo to use Posit Package Manager to freeze R package versions to
+# those available on 2023-10-30
+# https://packagemanager.posit.co/client/#/repos/2/overview
+# https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-30
+
+# set proper base image
+ARG R_VERS="4.3.1"
+FROM ghcr.io/rmi-pacta/workflow.pacta:main AS base
+
+# set Docker image labels
+LABEL org.opencontainers.image.source=https://github.com/RMI-PACTA/workflow.pacta.report
+LABEL org.opencontainers.image.description="Docker image to run PACTA"
+LABEL org.opencontainers.image.licenses=MIT
+LABEL org.opencontainers.image.title=""
+LABEL org.opencontainers.image.revision=""
+LABEL org.opencontainers.image.version=""
+LABEL org.opencontainers.image.vendor=""
+LABEL org.opencontainers.image.base.name=""
+LABEL org.opencontainers.image.ref.name=""
+LABEL org.opencontainers.image.authors=""
+
+# set apt-get to noninteractive mode
+ARG DEBIAN_FRONTEND="noninteractive"
+ARG DEBCONF_NOWARNINGS="yes"
+
+# install system dependencies
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+      libpng-dev=1.6.* \
+      libxt6=1:1.2.* \
+      pandoc=2.9.* \
+    && chmod -R a+rwX /root \
+    && rm -rf /var/lib/apt/lists/*
+
+# set frozen CRAN repo
+ARG CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-30"
+RUN echo "options(repos = c(CRAN = '$CRAN_REPO'), pkg.sysreqs = FALSE)" >> "${R_HOME}/etc/Rprofile.site" \
+      # install packages for dependency resolution and installation
+      && Rscript -e "install.packages('pak'); pak::pkg_install('renv')"
+
+FROM base AS install-pacta
+
+# copy in everything from this repo
+COPY DESCRIPTION /DESCRIPTION
+
+# PACTA R package tags
+ARG report_tag="/tree/main"
+ARG summary_tag="/tree/main"
+ARG utils_tag="/tree/main"
+
+ARG report_url="https://github.com/rmi-pacta/pacta.portfolio.report"
+ARG summary_url="https://github.com/rmi-pacta/pacta.executive.summary"
+ARG utils_url="https://github.com/rmi-pacta/pacta.portfolio.utils"
+
+# install R package dependencies
+RUN Rscript -e "\
+  gh_pkgs <- \
+    c( \
+      paste0('$report_url', '$report_tag'), \
+      paste0('$summary_url', '$summary_tag'), \
+      paste0('$utils_url', '$utils_tag') \
+    ); \
+  workflow_pkgs <- renv::dependencies('DESCRIPTION')[['Package']]; \
+  workflow_pkgs <- grep('^pacta[.]', workflow_pkgs, value = TRUE, invert = TRUE); \
+  pak::pak(c(gh_pkgs, workflow_pkgs)); \
+  "
+
+COPY . /
+
+# set default run behavior
+ENTRYPOINT ["/run-pacta.sh"]
+CMD ["input_dir/default_config.json"]

LICENSE

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+MIT License
+
+Copyright (c) 2023 RMI
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1 +1,52 @@
-# `workflow.pacta.report`
+# workflow.pacta.report
+
+# Description
+
+The Dockerfile in this repository creates an image containing a freshly
+cloned copy of `workflow.pacta.report`. It also installs the relevant PACTA R
+packages that it depends on.
+
+# Notes
+
+Running PACTA also requires pacta-data, which needs to be mounted into the
+container at run-time.
+
+# Using Docker images pushed to GHCR automatically by GH Actions
+
+``` {.bash}
+
+tag_name=main
+image_name=ghcr.io/rmi-pacta/workflow.pacta.report:$tag_name
+data_dir=~/Downloads/2022Q4_transition_monitor_inputs_2023-07-11/
+input_dir=./input_dir
+output_dir=./output_dir
+
+# Build
+docker build . -t $image_name
+
+# Run
+docker run --rm \
+  --network none \
+  --platform linux/amd64 \
+  --env LOG_LEVEL=DEBUG \
+  --mount type=bind,readonly,source=${data_dir},target=/pacta-data \
+  --mount type=bind,source=${output_dir},target=/output_dir \
+  --mount type=bind,source=${input_dir},target=/input_dir \
+  $image_name
+
+```
+
+```sh
+
+# Run R in container
+docker run -it --rm \
+  --network none \
+  --platform linux/amd64 \
+  --env LOG_LEVEL=TRACE \
+  --mount type=bind,readonly,source=${data_dir},target=/pacta-data \
+  --mount type=bind,source=${output_dir},target=/output_dir \
+  --mount type=bind,source=${input_dir},target=/input_dir \
+  --entrypoint R
+  $image_name
+
+```